Transform

Image processing operations leading to changes in the whole stack layout. For example, substack extraction, cropping or drift correction.

Modules performing alignment of images within a stack to account for sample drift or other motion.

DEPRECATED: Please use ExtractSubstack module.

Combine two or more image stacks into a single stack.

This is a candidate replacement for the original ConcatenateStacks.

Ensures 3D stacks (or 4D with multiple channels) are of the expected type (timeseries or Z-stack).

Crop an image in X and Y using pre-defined limits or limits based on the extents of objects in a collection.

Extract a substack from the specified input image in terms of channels, slices and frames.

Flips the order of slices in stack.

Extract a Z-substack from an input stack based on either manually-selected slices, or an automatically-calculated best-focus slice.

Focuses a Z-stack into a single plane using the StackFocuser ImageJ plugin.

Interpolates Z-axis of image to match XY spatial calibration

DEPRECATED: This Module has been superseeded by the more generalised "Concatenate stacks" Module.

This module duplicates an image into another, existing, image.

Applies independent X,Y and Z-axis scaling to an input image.